/* file: edf2mit.c G. Moody 16 October 1996
Last revised: 18 November 2008
-------------------------------------------------------------------------------
Convert EDF (European Data Format) file to MIT format header and signal files
Copyright (C) 1996-2004 George B. Moody
This program is free software; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation; either version 2 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program; if not, see <http://www.gnu.org/licenses/>.
You may contact the author by e-mail (wfdb@physionet.org) or postal mail
(MIT Room E25-505A, Cambridge, MA 02139 USA). For updates to this software,
please visit PhysioNet (http://www.physionet.org/).
_______________________________________________________________________________
*/
#include <stdio.h>
#include <wfdb/wfdb.h>
char *pname;
main(argc, argv)
int argc;
char **argv;
{
char buf[81], record[WFDB_MAXRNL+1], **vi, **vin;
double *sigpmax, *sigpmin, *sampfreq, spr, sps, gcd();
FILE *ifile = NULL;
int big_endian = 0, fpb, h, i, j, k, l, nsig, nosig = 0, *siglist = NULL,
*spb, tspb = 0, ispf = 0, tspf = 0, vflag = 0,
day, month, year, hour, minute, second;
long adcrange, *sigdmax, *sigdmin;
WFDB_Sample *vo, *vout;
WFDB_Siginfo *si, *so;
void help();
pname = argv[0];
record[0] = '\0';
for (i = 1; i < argc; i++) {
if (*argv[i] == '-') switch (argv[i][1]) {
case 'b': /* input is in big-endian byte order */
big_endian = 1;
break;
case 'h': /* show usage and quit */
help();
exit(0);
case 'i': /* file name follows */
if (++i < argc) {
if (!strcmp(argv[i], "-"))
ifile = stdin;
else {
ifile = fopen(argv[i], "rb");
if (ifile == NULL) {
fprintf(stderr, "%s: can't read %s\n", pname, argv[i]);
exit(1);
}
if (record[0] == 0) {
for (j = 0; j < WFDB_MAXRNL; j++) {
char c = argv[i][j];
if (('0' <= c && c <= '9') ||
('a' <= c && c <= 'z') ||
('A' <= c && c <= 'Z'))
record[j] = c;
else if (c == '.') break;
else record[j] = '_';
}
record[j] = '\0';
}
}
}
break;
case 'r': /* record name follows */
if (++i < argc)
strncpy(record, argv[i], WFDB_MAXRNL);
else {
fprintf(stderr, "%s: record name must follow -r\n", pname);
exit(1);
}
break;
case 's': /* signal list follows */
/* count the number of output signals */
for (j = 0; ++i < argc && *argv[i] != '-'; j++)
;
if (j == 0) {
(void)fprintf(stderr, "%s: signal list must follow -s\n",
pname);
exit(1);
}
/* allocate storage for the signal list */
if ((siglist=realloc(siglist, (nosig+j) * sizeof(int))) == NULL) {
(void)fprintf(stderr, "%s: insufficient memory\n", pname);
exit(2);
}
/* fill the signal list */
for (i -= j; i < argc && *argv[i] != '-'; )
siglist[nosig++] = atoi(argv[i++]);
i--;
break;
case 'v': /* select verbose mode */
vflag = 1;
break;
}
}
if (ifile == NULL) {
help();
exit(1);
}
if (record[0] == '\0' || newheader(record) < 0) {
fprintf(stderr, "\n");
help();
(void)fprintf(stderr,
"\nRun %s again, specifying a valid name for the output record,\n", argv[0]);
(void)fprintf(stderr,
"using the -r option as described above.\n\n");
(void)fprintf(stderr,
" Valid record names may include letters, digits, and underscores only.\n");
exit(1);
}
fread(buf, 1, 8, ifile);
/* Check to see that the input is an EDF file. (This check will detect
most but not all other types of files.) */
if (strncmp(buf, "0 ", 8)) {
(void)fprintf(stderr,
"%s: input does not appear to be EDF -- no conversion attempted.\n",
pname);
exit(2);
}
buf[8] = ' ';
for (j = 8; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag) printf("EDF version number: '%s'\n", buf);
fread(buf, 1, 80, ifile);
buf[80] = ' ';
for (j = 80; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag) printf("Patient ID: '%s'\n", buf);
fread(buf, 1, 80, ifile);
buf[80] = ' ';
for (j = 80; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag) printf("Recording ID: '%s'\n", buf);
fread(buf, 1, 8, ifile);
buf[8] = ' ';
for (j = 8; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag) printf("Recording date: '%s'\n", buf);
sscanf(buf, "%d%*c%d%*c%d", &day, &month, &year);
if (year < 1970) year += 1900;
if (year < 1970) year += 100; /* should work for a while */
fread(buf, 1, 8, ifile);
buf[8] = ' ';
for (j = 8; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag) printf("Recording time: '%s'\n", buf);
sscanf(buf, "%d%*c%d%*c%d", &hour, &minute, &second);
fread(buf, 1, 8, ifile);
buf[8] = ' ';
for (j = 8; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag) printf("Number of bytes in header record: '%s'\n", buf);
fread(buf, 1, 44, ifile);
buf[44] = ' ';
for (j = 44; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (j > 0)
if (vflag) printf("Free space: '%s'\n", buf);
fread(buf, 1, 8, ifile);
buf[8] = ' ';
for (j = 8; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag) printf("Number of data records: '%s'\n", buf);
fread(buf, 1, 8, ifile);
buf[8] = ' ';
for (j = 8; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag) printf("Duration of each data record in seconds: '%s'\n", buf);
sscanf(buf, "%lf", &spr);
if (spr <= 0.0) spr = 1.0;
fread(buf, 1, 4, ifile);
buf[4] = ' ';
for (j = 4; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag) printf("Number of signals: '%s'\n", buf);
sscanf(buf, "%d", &nsig);
if (nsig < 1) exit(1);
if ((si = calloc(nsig, sizeof(WFDB_Siginfo))) == NULL ||
(spb = calloc(nsig, sizeof(int))) == NULL ||
(sigdmax = calloc(nsig, sizeof(long))) == NULL ||
(sigdmin = calloc(nsig, sizeof(long))) == NULL ||
(sigpmax = calloc(nsig, sizeof(double))) == NULL ||
(sigpmin = calloc(nsig, sizeof(double))) == NULL ||
(sampfreq = calloc(nsig, sizeof(double))) == NULL) {
fprintf(stderr, "%s: insufficient memory\n", pname);
exit(2);
}
if (nosig == 0) { /* initialize signal list if necessary */
if ((siglist = malloc(nsig * sizeof(int))) == NULL) {
fprintf(stderr, "%s: insufficient memory\n", pname);
exit(2);
}
for ( ; nosig < nsig; nosig++)
siglist[nosig] = nosig;
}
else {
for (i = 0; i < nosig; i++) {
if (siglist[i] < 0 || siglist[i] >= nsig) {
fprintf(stderr,
"%s: invalid signal number, %d, in signal list\n",
pname, siglist[i]);
exit(1);
}
}
}
if ((so = malloc(nosig * sizeof(WFDB_Siginfo))) == NULL) {
fprintf(stderr, "%s: insufficient memory\n", pname);
exit(2);
}
for (i = 0; i < nsig; i++) {
fread(buf, 1, 16, ifile);
buf[16] = ' ';
for (j = 15; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag) printf("Signal %d label: '%s'\n", i, buf);
si[i].desc = (char *)malloc(strlen(buf)+1);
if (si[i].desc) strcpy(si[i].desc, buf);
}
for (i = 0; i < nsig; i++) {
fread(buf, 1, 80, ifile);
buf[80] = ' ';
for (j = 80; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag && j > 0)
printf("Signal %d transducer type: '%s'\n", i, buf);
}
for (i = 0; i < nsig; i++) {
fread(buf, 1, 8, ifile);
buf[8] = ' ';
for (j = 8; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag) printf("Signal %d physical dimension: '%s'\n", i, buf);
si[i].units = (char *)malloc(strlen(buf)+1);
if (si[i].units) strcpy(si[i].units, buf);
}
for (i = 0; i < nsig; i++) {
fread(buf, 1, 8, ifile);
buf[8] = ' ';
for (j = 8; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag) printf("Signal %d physical minimum: '%s'\n", i, buf);
sscanf(buf, "%lf", &sigpmin[i]);
}
for (i = 0; i < nsig; i++) {
fread(buf, 1, 8, ifile);
buf[8] = ' ';
for (j = 8; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag) printf("Signal %d physical maximum: '%s'\n", i, buf);
sscanf(buf, "%lf", &sigpmax[i]);
}
for (i = 0; i < nsig; i++) {
fread(buf, 1, 8, ifile);
buf[8] = ' ';
for (j = 8; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag) printf("Signal %d digital minimum: '%s'\n", i, buf);
sscanf(buf, "%ld", &sigdmin[i]);
}
for (i = 0; i < nsig; i++) {
fread(buf, 1, 8, ifile);
buf[8] = ' ';
for (j = 8; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag) printf("Signal %d digital maximum: '%s'\n", i, buf);
sscanf(buf, "%ld", &sigdmax[i]);
}
for (i = 0; i < nsig; i++) {
if (sigpmax[i] == sigpmin[i]) {
fprintf(stderr, "gain for signal %d is undefined\n", i);
continue;
}
si[i].adczero = (sigdmax[i]+1 + sigdmin[i])/2;
adcrange = sigdmax[i] - sigdmin[i];
si[i].gain = adcrange/(sigpmax[i] - sigpmin[i]);
for (j = 0; adcrange > 1; j++)
adcrange /= 2;
si[i].adcres = j;
si[i].baseline = sigdmax[i] - sigpmax[i]*si[i].gain + 1;
}
for (i = 0; i < nsig; i++) {
fread(buf, 1, 80, ifile);
buf[80] = ' ';
for (j = 80; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag && j > 0)
printf("Signal %d filtering information: '%s'\n", i, buf);
}
sps = 0.0;
for (i = 0; i < nsig; i++) {
fread(buf, 1, 8, ifile);
buf[8] = ' ';
for (j = 8; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag)
printf("Signal %d number of samples per record: '%s'\n", i, buf);
sscanf(buf, "%lf", &sampfreq[i]);
sscanf(buf, "%d", &spb[i]);
tspb += spb[i];
sampfreq[i] /= spr;
}
for (i = 0; i < nsig; i++) {
fread(buf, 1, 32, ifile);
buf[32] = ' ';
for (j = 32; j >= 0 && buf[j] == ' '; j--)
buf[j] = '\0';
if (vflag && j > 0)
printf("Signal %d free space: '%s'\n", i, buf);
}
/* Determine the base sampling frequency (the greatest common divisor of
all sampling frequencies for the signals in the signal list) */
sps = sampfreq[siglist[0]];
for (i = 1; i < nosig; i++)
if (sampfreq[siglist[i]] != sps)
sps = gcd(sps, sampfreq[siglist[i]]);
setsampfreq(sps);
sprintf(buf, "%02d:%02d:%02d %02d/%02d/%04d",
hour, minute, second, day, month, year);
setbasetime(buf);
sprintf(buf, "%s.dat", record);
for (i = 0; i < nosig; i++) {
si[siglist[i]].fname = buf;
si[siglist[i]].fmt = 16;
tspf += si[siglist[i]].spf = (int)(sampfreq[siglist[i]]/sps + 0.5);
so[i] = si[siglist[i]];
}
for (i = ispf = 0; i < nsig; i++)
ispf += (int)(sampfreq[i]/sps + 0.5);
fpb = spb[siglist[0]] / si[siglist[0]].spf;
if (vflag)
printf("\nOUTPUT:\nBase sampling frequency: %g Hz\n", sps);
for (i = j = k = 0; i < nosig; i++) {
if ((j = si[siglist[i]].spf) > k) {
k = j; l = siglist[i];
}
if (vflag)
printf(" Signal %d samples per second: %g (%d sample%s per frame)\n",
i, sampfreq[siglist[i]], j, j > 1 ? "s" : "");
}
vin = (char **)malloc(nsig * sizeof(char *));
vi = (char **)malloc(nosig * sizeof(char *));
for (i = 0; i < nsig; i++) {
vin[i] = (char *)malloc(spb[i] * 2);
}
vout = (WFDB_Sample *)malloc(tspf * sizeof(WFDB_Sample));
osigfopen(so, nosig);
while (1) {
for (i = 0; i < nsig; i++)
j = fread(vin[i], 2, spb[i], ifile);
if (j == 0) break;
for (j = 0; j < nosig; j++)
vi[j] = vin[siglist[j]];
for (i = 0; i < fpb; i++) {
vo = vout;
for (j = 0; j < nosig; j++)
for (k = 0; k < so[j].spf; k++) {
if (big_endian) {
h = *vi[j]++; /* high byte first */
l = *vi[j]++; /* then low byte */
}
else {
l = *vi[j]++; /* low byte first */
h = *vi[j]++; /* then high byte */
}
/* If a short int is not 16 bits, it may be necessary to
modify the next line for proper sign extension. */
*vo++ = ((int)((short)((h << 8) | (l &0xff))));
}
putvec(vout);
}
}
if (ifile != stdin) fclose(ifile);
newheader(record);
wfdbquit();
exit(0);
}
/* Calculate the greatest common divisor of x and y. This function uses
Euclid's algorithm, modified so that an exact answer is not required if the
(possibly non-integral) arguments do not have a common divisor that can be
represented exactly. */
double gcd(x, y)
double x, y;
{
double tol;
if (x > y) tol = 0.001*y;
else tol = 0.001*x;
while (1) {
if (x > y && x-y > tol) x -= y;
else if (y > x && y-x > tol) y -= x;
else return (x);
}
}
static char *help_strings[] = {
"usage: %s [OPTIONS ...]\n",
"where OPTIONS may include:",
" -b input is in big-endian byte order (default: little-endian)",
" -h print this usage summary",
" -i EDFILE read the specified European Data Format file",
" -r RECORD create the specified RECORD (default: input file name without",
" suffix)",
" -s SIGNAL [SIGNAL ...] copy only the specified signal(s) (use signal",
" numbers, beginning with zero; default: copy all signals)",
" -v print debugging output",
"This program reads an EDF file and creates MIT-format signal and header",
"files containing the same data.",
NULL
};
void help()
{
int i;
(void)fprintf(stderr, help_strings[0], pname);
for (i = 1; help_strings[i] != NULL; i++)
(void)fprintf(stderr, "%s\n", help_strings[i]);
}